Bio.SearchIO.BlastIO package
Submodules
Module contents
Bio.SearchIO support for BLAST+ output formats.
This module adds support for parsing BLAST+ outputs. BLAST+ is a rewrite of NCBI’s legacy BLAST (Basic Local Alignment Search Tool), based on the NCBI C++ toolkit. The BLAST+ suite is available as command line programs or on NCBI’s web page.
Bio.SearchIO.BlastIO was tested on the following BLAST+ flavors and versions:
flavors: blastn, blastp, blastx, tblastn, tblastx
versions: 2.2.22+, 2.2.26+
You should also be able to parse outputs from a local BLAST+ search or from NCBI’s web interface. Although the module was not tested against all BLAST+, it should still be able to parse these other versions’ outputs. Please submit a bug report if you stumble upon an unparsable file.
Some output formats from the BLAST legacy suite (BLAST+’s predecessor) may still be parsed by this module. However, results are not guaranteed. You may try to use the Bio.Blast module to parse them instead.
- More information about BLAST are available through these links:
Publication: http://www.biomedcentral.com/1471-2105/10/421
Web interface: http://blast.ncbi.nlm.nih.gov/
User guide: http://www.ncbi.nlm.nih.gov/books/NBK1762/
Supported Formats
Bio.SearchIO.BlastIO supports the following BLAST+ output formats:
XML - ‘blast-xml’ - parsing, indexing, writing
Tabular - ‘blast-tab’ - parsing, indexing, writing
blast-xml
The blast-xml parser follows the BLAST XML DTD written here: http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod.dtd
It provides the following attributes for each SearchIO object:
Object |
Attribute |
XML Element |
---|---|---|
QueryResult |
target |
BlastOutput_db |
program |
BlastOutput_program |
|
reference |
BlastOutput_reference |
|
version |
BlastOutput_version [1] |
|
description |
Iteration_query-def |
|
id |
Iteration_query-ID |
|
seq_len |
Iteration_query-len |
|
param_evalue_threshold |
Parameters_expect |
|
param_entrez_query |
Parameters_entrez-query |
|
param_filter |
Parameters_filter |
|
param_gap_extend |
Parameters_gap-extend |
|
param_gap_open |
Parameters_gap-open |
|
param_include |
Parameters_include |
|
param_matrix |
Parameters_matrix |
|
param_pattern |
Parameters_pattern |
|
param_score_match |
Parameters_sc-match |
|
param_score_mismatch |
Parameters_sc-mismatch |
|
stat_db_num |
Statistics_db-num |
|
stat_db_len |
Statistics_db-len |
|
stat_eff_space |
Statistics_eff-space |
|
stat_entropy |
Statistics_entropy |
|
stat_hsp_len |
Statistics_hsp-len |
|
stat_kappa |
Statistics_kappa |
|
stat_lambda |
Statistics_lambda |
|
Hit |
accession |
Hit_accession |
description |
Hit_def |
|
id |
Hit_id |
|
seq_len |
Hit_len |
|
HSP |
bitscore |
Hsp_bit-score |
density |
Hsp_density |
|
evalue |
Hsp_evalue |
|
gap_num |
Hsp_gaps |
|
ident_num |
Hsp_identity |
|
pos_num |
Hsp_positive |
|
bitscore_raw |
Hsp_score |
|
HSPFragment (also via HSP) |
aln_span |
Hsp_align-len |
hit_frame |
Hsp_hit-frame |
|
hit_start |
Hsp_hit-from |
|
hit_end |
Hsp_hit-to |
|
hit |
Hsp_hseq |
|
aln_annotation |
Hsp_midline |
|
pattern_start |
Hsp_pattern-from |
|
pattern_end |
Hsp_pattern-to |
|
query_frame |
Hsp_query-frame |
|
query_start |
Hsp_query-from |
|
query_end |
Hsp_query-to |
|
query |
Hsp_qseq |
You may notice that in BLAST XML files, sometimes BLAST replaces your true sequence ID with its own generated ID. For example, the query IDs become ‘Query_1’, ‘Query_2’, and so on. While the hit IDs sometimes become ‘gnl|BL_ORD_ID|1’, ‘gnl|BL_ORD_ID|2’, and so on. In these cases, BLAST lumps the true sequence IDs together with their descriptions.
The blast-xml parser is aware of these modifications and will attempt to extract the true sequence IDs out of the descriptions. So when accessing QueryResult or Hit objects, you will use the non-BLAST-generated IDs.
This behavior on the query IDs can be disabled using the ‘use_raw_query_ids’ parameter while the behavior on the hit IDs can be disabled using the ‘use_raw_hit_ids’ parameter. Both are boolean values that can be supplied to SearchIO.read or SearchIO.parse, with the default values set to ‘False’.
In any case, the raw BLAST IDs can always be accessed using the query or hit object’s ‘blast_id’ attribute.
The blast-xml write function also accepts ‘use_raw_query_ids’ and ‘use_raw_hit_ids’ parameters. However, note that the default values for the writer are set to ‘True’. This is because the writer is meant to mimic native BLAST result as much as possible.
blast-tab
The default format for blast-tab support is the variant without comments (-m 6 flag). Commented BLAST tabular files may be parsed, indexed, or written using the keyword argument ‘comments’ set to True:
>>> # blast-tab defaults to parsing uncommented files
>>> from Bio import SearchIO
>>> uncommented = 'Blast/tab_2226_tblastn_004.txt'
>>> qresult = SearchIO.read(uncommented, 'blast-tab')
>>> qresult
QueryResult(id='gi|11464971:4-101', 5 hits)
>>> # set the keyword argument to parse commented files
>>> commented = 'Blast/tab_2226_tblastn_008.txt'
>>> qresult = SearchIO.read(commented, 'blast-tab', comments=True)
>>> qresult
QueryResult(id='gi|11464971:4-101', 5 hits)
For uncommented files, the parser defaults to using BLAST’s default column ordering: ‘qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore’.
If you want to parse an uncommented file with a customized column order, you can use the ‘fields’ keyword argument to pass the custom column order. The names of the column follow BLAST’s naming. For example, ‘qseqid’ is the column for the query sequence ID. These names may be passed either as a Python list or as a space-separated strings.
>>> # pass the custom column names as a Python list
>>> fname = 'Blast/tab_2226_tblastn_009.txt'
>>> custom_fields = ['qseqid', 'sseqid']
>>> qresult = next(SearchIO.parse(fname, 'blast-tab', fields=custom_fields))
>>> qresult
QueryResult(id='gi|16080617|ref|NP_391444.1|', 3 hits)
>>> # pass the custom column names as a space-separated string
>>> fname = 'Blast/tab_2226_tblastn_009.txt'
>>> custom_fields = 'qseqid sseqid'
>>> qresult = next(SearchIO.parse(fname, 'blast-tab', fields=custom_fields))
>>> qresult
QueryResult(id='gi|16080617|ref|NP_391444.1|', 3 hits)
You may also use the ‘std’ field name as an alias to BLAST’s default 12 columns, just like when you run a command line BLAST search.
Note that the ‘fields’ keyword argument will be ignored if the parsed file is commented. Commented files have their column ordering stated explicitly in the file, so there is no need to specify it again in SearchIO.
‘comments’ and ‘fields’ keyword arguments are both applicable for parsing, indexing, and writing.
blast-tab provides the following attributes for each SearchIO objects:
Object |
Attribute |
Column name |
---|---|---|
QueryResult |
accession |
qacc |
accession_version |
qaccver |
|
gi |
qgi |
|
seq_len |
qlen |
|
id |
qseqid |
|
Hit |
accession |
sacc |
accession_version |
sacc_ver |
|
gi |
sgi |
|
gi_all |
sallgi |
|
id_all |
sallseqid |
|
seq_len |
slen |
|
id |
sseqid |
|
HSP |
bitscore |
bitscore |
btop |
btop |
|
evalue |
evalue |
|
gapopen_num |
gapopen |
|
gap_num |
gaps |
|
ident_num |
nident |
|
ident_pct |
pident |
|
mismatch_num |
mismatch |
|
pos_pct |
ppos |
|
pos_num |
positive |
|
bitscore_raw |
score |
|
HSPFragment (also via HSP) |
frames |
frames [2] |
aln_span |
length |
|
query_end |
qend |
|
query_frame |
qframe |
|
query |
qseq |
|
query_start |
qstart |
|
hit_end |
send |
|
hit_frame |
sframe |
|
hit |
sseq |
|
hit_start |
sstart |
If the parsed file is commented, the following attributes may be available as well:
Object |
Attribute |
Value |
---|---|---|
QueryResult |
description |
query description |
fields |
columns in the output file |
|
program |
BLAST flavor |
|
rid |
remote search ID |
|
target |
target database |
|
version |
BLAST version |